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Abstract: Here we study the morphology and the optical properties of assemblies made of small (17 nm) gold nanoparticles (AuNPs) directly on silicon wafers coated with (3-aminopropyl)trimethoxysilane (APTES). We employed aliphatic 1,6-hexanedithiol (HDT) molecules to cross-link AuNPs during a two-stage precipitation procedure. The first immersion of the wafer in AuNP colloidal solution led mainly to the attachment of single particles with few inclusions of dimers and small aggregates. After the functionalization of precipitated NPs with HDT and after the second immersion in the colloidal solution of AuNP, we detected a sharp rise in the number of aggregates compared to single AuNPs and their dimers. The lateral size of the aggregates was about 100 nm, while some of them were larger than 1μm. We propose that the uncompensated dipole moment of the small aggregates appeared after the first precipitation and acts further as the driving force accelerating their further growth on the surface during the second precipitation. By having such inhomogeneous surface coating, the X-ray reciprocal space maps and modulation polarimetry showed well-distinguished signals from the single AuNPs and their dimers. From these observations, we concluded that the contribution from aggregated AuNPs does not hamper the detection and investigation of plasmonic effects for AuNP dimers. Meantime, using unpolarized and polarized light spectroscopy, the difference in the optical signals between the dimers, being formed because of self-aggregation and the one being cross-linked by means of HDT, was not detected.